X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;fp=engine.cpp;h=24adcb53b59f39f049269d74b4da953a5f387262;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
new file mode 100644
index 0000000..24adcb5
--- /dev/null
+++ b/engine.cpp
@@ -0,0 +1,615 @@
+/*
+ *  engine.cpp
+ *  
+ *
+ *  Created by Pat Schloss on 8/15/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ *  There's a TON of duplicated code between InteractEngine and BatchEngine
+ *  I couldn't figure out how to transition between ifstream (batch) and cin (interact)
+ *  Fix later, don't have time now.
+ *
+ */
+
+
+#include "engine.hpp"
+
+/***********************************************************************/
+Engine::Engine(){
+	try {
+		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "Engine");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string Engine::findMothursPath(){
+	try { 
+		
+		string envPath = getenv("PATH");
+		string mothurPath = "";
+		
+		//delimiting path char
+		char delim;
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+			delim = ':';
+		#else
+			delim = ';';
+		#endif
+		
+		//break apart path variable by ':'
+		vector<string> dirs;
+		mout->splitAtChar(envPath, dirs, delim);
+		
+		//get path related to mothur
+		for (int i = 0; i < dirs.size(); i++) {
+			//to lower so we can find it
+			string tempLower = "";
+			for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
+			
+			//is this mothurs path?
+			if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
+		}
+		
+		if (mothurPath != "") {
+			//add mothur so it looks like what argv would look like
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				mothurPath += "/mothur";
+			#else
+				mothurPath += "\\mothur";
+			#endif
+		}else {
+			//okay mothur is not in the path, so the folder mothur is in must be in the path
+			//lets find out which one
+			
+			//get path related to mothur
+			for (int i = 0; i < dirs.size(); i++) {
+								
+				//is this mothurs path?
+				ifstream in;
+				string tempIn = dirs[i];
+				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+					tempIn += "/mothur";
+				#else
+					tempIn += "\\mothur";
+				#endif
+				mout->openInputFile(tempIn, in, "");
+				
+				//if this file exists
+				if (in) { in.close(); mothurPath = tempIn;  break;  }
+			}
+		}
+		
+		return mothurPath;
+		
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "findMothursPath");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+InteractEngine::InteractEngine(string path){
+
+	
+	string temppath = path.substr(0, (path.find_last_of("othur")-5));
+	
+	//this will happen if you set the path variable to contain mothur's exe location
+	if (temppath == "") { path = findMothursPath(); }
+	
+	mout->argv = path;
+}
+
+/***********************************************************************/
+
+InteractEngine::~InteractEngine(){}
+
+/***********************************************************************/
+//This function allows the user to input commands one line at a time until they quit.
+//If the command is garbage it does nothing.
+bool InteractEngine::getInput(){
+	try {
+		string input = "";
+		string commandName = "";
+		string options = "";
+		int quitCommandCalled = 0;
+		
+		while(quitCommandCalled != 1){
+
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
+			mout->mothurOutEndLine();
+			
+			input = getCommand();	
+			mout->mothurOutEndLine();	
+			
+			if (mout->control_pressed) { input = "quit()"; }
+			
+			//allow user to omit the () on the quit command
+			if (input == "quit") { input = "quit()"; }
+
+			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+		
+			CommandOptionParser parser(input);
+			commandName = parser.getCommandString();
+	
+			options = parser.getOptionString();
+			
+			if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					//cout << pid << " is in execute " << commandName << endl;
+					#endif
+					//executes valid command
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+							
+					Command* command = cFactory->getCommand(commandName, options);
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
+							
+					//if we aborted command
+					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
+		}	
+		return 1;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "InteractEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string Engine::getCommand()  {
+	try {
+	
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+			#ifdef USE_READLINE
+				char* nextCommand = NULL;
+				nextCommand = readline("mothur > ");
+				
+				if(nextCommand != NULL) {  add_history(nextCommand);  }	
+				else{ //^D causes null string and we want it to quit mothur
+					nextCommand = strdup("quit");
+					mout->mothurOut(nextCommand);
+				}	
+				
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				return nextCommand;
+			#else
+				string nextCommand = "";
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
+				return nextCommand;
+			#endif
+		#else
+				string nextCommand = "";
+				
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog(toString(nextCommand));
+				
+				return nextCommand;
+		#endif
+	
+						
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "getCommand");
+		exit(1);
+	}
+}
+/***********************************************************************/
+//This function opens the batchfile to be used by BatchEngine::getInput.
+BatchEngine::BatchEngine(string path, string batchFileName){
+	try {
+	
+		openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
+		
+		string temppath = path.substr(0, (path.find_last_of("othur")-5));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { path = findMothursPath(); }
+		
+		mout->argv = path;
+				
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+BatchEngine::~BatchEngine(){	}
+
+/***********************************************************************/
+//This Function allows the user to run a batchfile containing several commands on Dotur
+bool BatchEngine::getInput(){
+	try {
+		//check if this is a valid batchfile
+		if (openedBatch == 1) {  
+			mout->mothurOut("unable to open batchfile");  
+			mout->mothurOutEndLine();
+			return 1; 
+		}
+	
+		string input = "";
+		string commandName = "";
+		string options = "";
+		
+		//CommandFactory cFactory;
+		int quitCommandCalled = 0;
+	    int count = 0;
+		while(quitCommandCalled != 1){
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
+			input = getNextCommand(inputBatchFile);
+			count++;
+			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+
+			
+			
+			if (input[0] != '#') {
+				
+				mout->mothurOutEndLine();
+				mout->mothurOut("mothur > " + input);
+				mout->mothurOutEndLine();
+							
+				if (mout->control_pressed) { input = "quit()"; }
+				
+				//allow user to omit the () on the quit command
+				if (input == "quit") { input = "quit()"; }
+
+				CommandOptionParser parser(input);
+				commandName = parser.getCommandString();
+				options = parser.getOptionString();
+										
+				if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+//cout << pid << " is here " << commandName << '\t' << count << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
+					//executes valid command
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
+							
+					Command* command = cFactory->getCommand(commandName, options);
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
+							
+					//if we aborted command
+					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
+				
+			}
+			mout->gobble(inputBatchFile);
+		}
+		
+		inputBatchFile.close();
+		return 1;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+	try {
+			
+		string nextcommand = "";
+		
+		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+		else { nextcommand = mout->getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+/***********************************************************************/
+//This function opens the batchfile to be used by BatchEngine::getInput.
+ScriptEngine::ScriptEngine(string path, string commandString){
+	try {
+		
+		//remove quotes
+		listOfCommands = commandString.substr(1, (commandString.length()-1));
+		
+		string temppath = path.substr(0, (path.find_last_of("othur")-5));
+
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { path = findMothursPath(); }
+		
+		mout->argv = path;
+				
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "ScriptEngine");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+ScriptEngine::~ScriptEngine(){ 	}
+
+/***********************************************************************/
+//This Function allows the user to run a batchfile containing several commands on mothur
+bool ScriptEngine::getInput(){
+	try {
+			
+		string input = "";
+		string commandName = "";
+		string options = "";
+		
+		
+		//CommandFactory cFactory;
+		int quitCommandCalled = 0;
+	
+		while(quitCommandCalled != 1){
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
+			input = getNextCommand(listOfCommands);	
+			
+			if (input == "") { input = "quit()"; }
+			
+			if (mout->gui) {
+				if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
+				else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
+				else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
+			}else{
+				mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
+			}
+			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+			
+			
+			if (mout->control_pressed) { input = "quit()"; }
+				
+			//allow user to omit the () on the quit command
+			if (input == "quit") { input = "quit()"; }
+
+			CommandOptionParser parser(input);
+			commandName = parser.getCommandString();
+			options = parser.getOptionString();
+										
+			if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid, numProcesses;
+						
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
+					
+//cout << pid << " is here " << commandName  << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+							//cout << pid << " is in execute" << endl;	
+					#endif
+					//executes valid command
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
+					Command* command = cFactory->getCommand(commandName, options);
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
+					
+					//if we aborted command
+					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+							
+					mout->control_pressed = 0;
+					mout->executing = false;
+									
+					#ifdef USE_MPI
+					//cout << pid << " is done in execute" << endl;
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
+
+			
+		}
+		
+		return 1;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string ScriptEngine::getNextCommand(string& commandString) {
+	try {
+		
+		string nextcommand = "";
+		int count = 0;
+		bool ignoreSemiColons = false;
+		
+		//go through string until you reach ; or end
+		while (count < commandString.length()) { 
+			
+			 //you want to ignore any ; until you reach the next '
+			if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  } 
+			else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  } 
+				
+			if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
+			else {		nextcommand += commandString[count];	}
+			
+			count++;
+		}
+		
+		//if you are not at the end
+		if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
+		else { commandString = ""; }
+				
+		
+		//get rid of spaces in between commands if any
+		if (commandString.length() > 0) {
+			while (commandString[0] == ' ') {  
+				commandString = commandString.substr(1,commandString.length());
+				if (commandString.length() == 0) {  break;  }
+			}
+		}
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
+		exit(1);
+	}
+}
+/***********************************************************************/